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MACS2 Python3 support is hopefully coming... macs3-project/MACS#242 (comment) (though there have been threads around this since 2017, so not sure when..)
Would be nice to add the IDR analysis that is currently carried out by the ENCODE pipelines:
https://github.com/kundajelab/atac-seq-pipeline
https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P7KOMxTOP-HiNoIvL1VcBt8/edit
Another implementation in NF:
https://github.com/DoaneAS/atacflow
ENCODE ATAC-seq Guidelines:
https://www.encodeproject.org/atac-seq/
Amongst other things, this will probably also involve creating pseudo-replicates by merging and equally sampling alignments across replicates.
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